PDBize: do not put chains marked as 'polymer' in the ligand chain.

CHANGELOG.txt

@@ -2,7 +2,9 @@ Changes in Release 2.2.x
 --------------------------------------------------------------------------------
 
  * Removed GUI components in containers
- * DSSP 4.0 support in DSSP binding (https://github.com/PDB-REDO/dssp) 
+ * DSSP 4.0 support in DSSP binding (https://github.com/PDB-REDO/dssp)
+ * mol.alg.PDBize does not turn plain polymer chains (not marked peptide or
+   nucleotide) into ligand chains anymore
  * Several minor bug fixes and improvements.
 
 Changes in Release 2.2.0

modules/mol/alg/src/pdbize.cc

@@ -88,7 +88,9 @@ void PDBize::Add(EntityView asu, const geom::Mat4List& transforms,
       if ((chain.IsPolypeptide() && chain_length >= peptide_min_size_) ||
           (chain.IsPolynucleotide() && chain_length >= nucleicacid_min_size_) ||
           ((chain.IsOligosaccharide() || chain.IsPolysaccharide()) &&
-           chain_length >= saccharide_min_size_)) {
+           chain_length >= saccharide_min_size_) ||
+          (chain.GetType() == CHAINTYPE_POLY && chain_length >= peptide_min_size_ &&
+          chain_length >= nucleicacid_min_size_)) {
         if (*curr_chain_name_ == 0) {
           throw std::runtime_error("running out of chain names");
         }